Search for Variation information by Variation ID:
Detailed information for vg1105159835:
| Variant ID: vg1105159835 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159835 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCTTCCTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGAC[C/T]
TCTTCTTCCTCCTCCTGTCACGCCGCCCTGTCCGAGCAGCAGATCCGGGGACGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAGGTCCATGCCTC
Reverse complement sequence
GAGGCATGGACCTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCGTCCCCGGATCTGCTGCTCGGACAGGGCGGCGTGACAGGAGGAGGAAGAAGA[G/A]
GTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAGGAAGCC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.60% | 0.10% | 10.28% | 32.99% | NA |
| All Indica | 2759 | 42.30% | 0.00% | 13.85% | 43.89% | NA |
| All Japonica | 1512 | 85.80% | 0.00% | 3.84% | 10.38% | NA |
| Aus | 269 | 41.60% | 0.00% | 7.06% | 51.30% | NA |
| Indica I | 595 | 25.50% | 0.00% | 5.71% | 68.74% | NA |
| Indica II | 465 | 32.70% | 0.00% | 9.68% | 57.63% | NA |
| Indica III | 913 | 56.40% | 0.00% | 23.99% | 19.61% | NA |
| Indica Intermediate | 786 | 44.10% | 0.00% | 10.69% | 45.17% | NA |
| Temperate Japonica | 767 | 90.10% | 0.00% | 0.91% | 9.00% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 6.94% | 11.11% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.00% | 6.64% | 13.28% | NA |
| VI/Aromatic | 96 | 52.10% | 7.30% | 19.79% | 20.83% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 8.89% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159835 | C -> T | LOC_Os11g09660.1 | missense_variant ; p.Arg429Lys; MODERATE | nonsynonymous_codon ; R429K | Average:5.072; most accessible tissue: Callus, score: 8.148 | benign  |
0.424 |
DELETERIOUS | 0.04 |
| vg1105159835 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.072; most accessible tissue: Callus, score: 8.148 | N | N | N | N |